MSY Breakpoint Mapper, a database of sequence-tagged sites useful in defining naturally occurring deletions in the human Y chromosome

Y chromosome deletions arise frequently in human populations, where they cause sex reversal and Turner syndrome and predispose individuals to infertility and germ cell cancer. Knowledge of the nucleotide sequence of the male-specific region of the Y chromosome (MSY) makes it possible to precisely demarcate such deletions and the repertoires of genes lost, offering insights into mechanisms of deletion and the molecular etiologies of associated phenotypes. Such deletion mapping is usually conducted using polymerase chain reaction (PCR) assays for the presence or absence of a series of Y-chromosomal DNA markers, or sequence-tagged sites (STSs). In the course of mapping intact and aberrant Y chromosomes during the past two decades, we and our colleagues have developed robust PCR assays for 1287 Y-specific STSs. These PCR assays amplify 1698 loci at an average spacing of <14 kb across the MSY euchromatin. To facilitate mapping of deletions, we have compiled a database of these STSs, MSY Breakpoint Mapper (http://breakpointmapper.wi.mit.edu/). When queried, this online database provides regionally targeted catalogs of STSs and nearby genes. MSY Breakpoint Mapper is useful for efficiently and systematically defining the breakpoint(s) of virtually any naturally occurring Y chromosome deletion.National Institutes of Health (U.S.)Howard Hughes Medical Institut

Loss of Olfactory Receptor Genes Coincides with the Acquisition of Full Trichromatic Vision in Primates

Olfactory receptor (OR) genes constitute the molecular basis for the sense of smell and are encoded by the largest gene family in mammalian genomes. Previous studies suggested that the proportion of pseudogenes in the OR gene family is significantly larger in humans than in other apes and significantly larger in apes than in the mouse. To investigate the process of degeneration of the olfactory repertoire in primates, we estimated the proportion of OR pseudogenes in 19 primate species by surveying randomly chosen subsets of 100 OR genes from each species. We find that apes, Old World monkeys and one New World monkey, the howler monkey, have a significantly higher proportion of OR pseudogenes than do other New World monkeys or the lemur (a prosimian). Strikingly, the howler monkey is also the only New World monkey to possess full trichromatic vision, along with Old World monkeys and apes. Our findings suggest that the deterioration of the olfactory repertoire occurred concomitant with the acquisition of full trichromatic color vision in primates

New York: the animated city

The urban landscape of New York City is one that is familiar to many, but, through the medium of animation, this familiarity has been consistently challenged. Often metamorphic, and always meticulously constructed, animated imagery encourages reflective thinking. Focusing on the themes of construction, destruction, and interactivity, this article seeks to cast critical light upon the animated double life that New York City has lived through the following moving image texts: Disney’s Fantasia 2000 (1999), Patrick Jean’s computer-generated short Pixels (2009), and Rockstar Games’ open-world blockbuster Grand Theft Auto IV (2008)

Conservatism in Laboratory Microsocieties: Unpredictable Payoffs Accentuate Group-Specific Traditions

Theoretical work predicts that individuals should strategically increase their reliance on social learning when individual learning would be costly or risky, or when the payoffs for individually-learned behaviors are uncertain. Using a method known to elicit cumulative cultural evolution in the laboratory, we investigated the degree of within-group similarity, and between-group variation, in design choices made by participants under conditions of varying uncertainty about the likely effectiveness of those designs. Participants were required to build a tower from spaghetti and modeling clay, their goal being to build the tower as high as possible. In one condition, towers were measured immediately on completion, and therefore participants were able to judge the success of their design during building. In the other condition, participants’ towers were measured five minutes after completion, following a deliberate attempt to test the tower’s stability, making it harder for participants to judge whether an innovative solution was liable to result in a good score on the final measurement. Cultural peculiarity (i.e. the extent to which a design could be identified as belonging to a particular chain) was stronger in the delayed measure condition, indicating that participants were placing greater reliance on social learning. Furthermore in this condition there was only very weak evidence of successive improvement in performance over learner generations, whereas in the immediate measure condition there was a clear effect of steadily increasing scores on the goal measurement. Increasing the risk associated with learning for oneself may favor the development of arbitrary traditions

Questioning short-term memory and its measurement: why digit span measures long-term associative learning

Traditional accounts of verbal short-term memory explain differences in performance for different types of verbal material by reference to inherent characteristics of the verbal items making up memory sequences. The role of previous experience with sequences of different types is ostensibly controlled for either by deliberate exclusion or by presenting multiple trials constructed from different random permutations

Experimental models for testing hypotheses about cumulative cultural evolution

The rapid appearance (over evolutionary time) of the cognitive skills and complex inventions of modern humans has been attributed to “cumulative cultural evolution” (henceforth CCE), the accumulation of knowledge and skills over generations. To date, researchers have only been able to speculate about the reasons for the apparent absence of this phenomenon in nonhumans, and it has not been possible to test hypotheses regarding the mechanisms underlying it. Here we show that it is possible to demonstrate CCE under laboratory conditions, by simulating generational succession through the repeated removal and replacement of human participants within experimental groups. We created “microsocieties” in which participants were instructed to complete simple tasks using everyday materials. In one of our procedures, participants were instructed to build a paper aeroplane which flew as far as possible, and in the other, they were instructed to construct a tower of spaghetti which was as tall as possible. We show that, in both cases, information accumulates within the groups such that later generations produce designs which are more successful than earlier ones. These methods offer researchers a window to understanding CCE, allowing for experimental manipulation and hypothesis testing

The Precision Array for Probing the Epoch of Reionization: 8 Station Results

We are developing the Precision Array for Probing the Epoch of Reionization (PAPER) to detect 21cm emission from the early Universe, when the first stars and galaxies were forming. We describe the overall experiment strategy and architecture and summarize two PAPER deployments: a 4-antenna array in the low-RFI environment of Western Australia and an 8-antenna array at our prototyping site in Green Bank, WV. From these activities we report on system performance, including primary beam model verification, dependence of system gain on ambient temperature, measurements of receiver and overall system temperatures, and characterization of the RFI environment at each deployment site. We present an all-sky map synthesized between 139 MHz and 174 MHz using data from both arrays that reaches down to 80 mJy (4.9 K, for a beam size of 2.15e-5 steradians at 154 MHz), with a 10 mJy (620 mK) thermal noise level that indicates what would be achievable with better foreground subtraction. We calculate angular power spectra ($C_\ell$) in a cold patch and determine them to be dominated by point sources, but with contributions from galactic synchrotron emission at lower radio frequencies and angular wavemodes. Although the cosmic variance of foregrounds dominates errors in these power spectra, we measure a thermal noise level of 310 mK at $\ell=100$ for a 1.46-MHz band centered at 164.5 MHz. This sensitivity level is approximately three orders of magnitude in temperature above the level of the fluctuations in 21cm emission associated with reionization.Comment: 13 pages, 14 figures, submitted to AJ. Revision 2 corrects a scaling error in the x axis of Fig. 12 that lowers the calculated power spectrum temperatur

Cluster M Mycobacteriophages Bongo, PegLeg, and Rey with Unusually Large Repertoires of tRNA Isotopes

Genomic analysis of a large set of phages infecting the common hostMycobacterium smegmatis mc2155 shows that they span considerable genetic diversity. There are more than 20 distinct types that lack nucleotide similarity with each other, and there is considerable diversity within most of the groups. Three newly isolated temperate mycobacteriophages, Bongo, PegLeg, and Rey, constitute a new group (cluster M), with the closely related phages Bongo and PegLeg forming subcluster M1 and the more distantly related Rey forming subcluster M2. The cluster M mycobacteriophages have siphoviral morphologies with unusually long tails, are homoimmune, and have larger than average genomes (80.2 to 83.7 kbp). They exhibit a variety of features not previously described in other mycobacteriophages, including noncanonical genome architectures and several unusual sets of conserved repeated sequences suggesting novel regulatory systems for both transcription and translation. In addition to containing transfer-messenger RNA and RtcB-like RNA ligase genes, their genomes encode 21 to 24 tRNA genes encompassing complete or nearly complete sets of isotypes. We predict that these tRNAs are used in late lytic growth, likely compensating for the degradation or inadequacy of host tRNAs. They may represent a complete set of tRNAs necessary for late lytic growth, especially when taken together with the apparent lack of codons in the same late genes that correspond to tRNAs that the genomes of the phages do not obviously encode